Glowing bear

27th October 2016

Wibo Pipping – The Hyve

Glowing bearA modern user interface for tranSMART using the REST API

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Agenda/Overview

● IMI Translocation

● Principles for the new UI

● Glowing bear

○ Design

○ Current status

○ Roadmap

● Questions

IMI TranslocationNew drugs 4 bad bugs

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Translocation

● Part of the IMI antimicrobial resistance programme

● Integrate existing knowledge

○ Preclinical data

○ Clinical data

● Extend the REST API

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Translocation - Role in project

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Translocation - features

● Extended tranSMART REST API

● Improved R client

○ Reduced data download overhead

○ Extended constraints for data download

● Started work on new UI - Glowing bear

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Translocation - New UI

● cBioPortal inspired

● Utilizes the REST API

● Well received

● Use cases provided by

● tranSMART community

PrinciplesCurrent UI and glowing bear

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Current tranSMART UI● User experience:

○ Outdated look and feel

○ Steep learning curve

○ Feedback not always clear

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Current tranSMART UI

● Technological debt:

○ Old fashioned server architecture

○ No separation of concerns

○ No test coverage

Cur

rent

cod

e qu

ality

→

Time to implement new feature →

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Glowing bear - Goals

● Replace old UI for all common use cases

● Improve cohort selection to improve usability

● Improve user experience

● Leverage new functionality and improved REST API

build in 17.1 project

○ Longitudinal data

○ Modifier support

○ Cross study support

○ Data linking to third parties (i.e. Arvados)

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Principles

● Responsive

○ Feedback to the user

● Informative

○ Insight into what data the user has

● Intuitive

○ Gradual learning curve

○ Low threshold to start

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Responsive

● Feedback

○ Early

○ Correct location

○ Clear

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Informative

● Insight in what the data has to offer

○ Ranges and distributions

○ Update figures when selecting data

● Maintain information flow through the system

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Intuitive

● Flatten learning curve

● Lower threshold for new users

● Dynamic transition from simple to more complex use

cases

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Glowing bear - design part 1

● Interactive dynamic web application

○ cBioPortal inspired

● Separation of concerns

○ Modular system

○ Separate back-end and front-end

TranSMART CoreDB + CoreAPI

REST API

Glowing bear

● Processing power● long running jobs● data storage

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Glowing bear - design part 2

● Separation of concerns

○ Also in the front-end itself

● Plugin architecture

○ SmartR

○ Genome browser?

○ …. ?

● Why?

○ Simplify development and maintenance

Glowing bear

SmartR

Plugin X

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Glowing bear - design part 3 ● Produced code has to have tests

○ Avoid regressions

○ Maintain quality of the product

● Current UI code base has a 0.00% test coverage

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Recent additions

● Improved cohort selection

○ Supports up to 2 cohorts

○ Cohort grid

● Save and retrieve cohorts

● Plugin architecture

○ SmartR support

● Searching on study level

● metadata

Glowing bearIn development and Roadmap

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Currently in development

● Data export

○ Adjusting REST API for support

● Longitudinal data

● Improved study selection

● File linking

● Cross study support

● Improve smartR workflow

● Extend searching concepts/metadata

● Frontpage - study changes statistics

● Advanced visualisations

● Notebook support

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Planned roadmap - features

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Planned roadmap

● Longitudinal data

○ Waiting for 17.1 Backend implementation

○ Support temporal relations in data queries

○ UI component in design phase

● Improve smartR workflow

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Planned roadmap

● Improved study selection

○ Controlled vocabulary

○ Genes

● Frontpage - study changes statistics

○ Recently loaded studies

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Planned roadmap

● File linking

○ Arvados

● Cross study support

● Extend searching concepts/metadata

○ Searching on concepts

● Advanced visualisations

○ Line graphs with data transformation

● Notebook support

○ Adding custom analysis

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Want to contribute/test?

● Get in touch with us to become a tester/developer or

adopt a feature:

○ [email protected]

○ [email protected]

○ [email protected]

Questions